Stuffer-free multiplex ligation-dependent probe amplification technology for identifying the copy number variation markers associated with the risk of SLE
Yeun-Jun Chung, Seon-Hee Yim and Seung-Hyun Jung
The Catholic University of Korea, Korea
: J Diagnos Tech Biomed Anal
Abstract
Copy number variation (CNV) is one of the major components of human genetic variations and it is thought to contribute to inter-individual differences in diverse phenotypes. Several CNVs have been suggested to be associated with systemic lupus erythematosus (SLE) through the target gene approach; however, genome-wide feature of CNVs in the risk of SLE has not well studied. Recently, our group studied the genome-wide CNVs with 964 SLE patients and 711 normal control individuals by whole genome SNP array analysis, and identified three CNVs of RABGAP1L, 10q21.3, and C4 associated with the risk of SLE in Korean Women (Arthritis and Rheumatism 65:1055-63 2013). For the multiplex detection of the 3 CNVs, we adopted a stuffer-free multiplex ligation-dependent probe amplification based on conformation-sensitive capillary electrophoresis, which we developed previously (MLPA-CE-SSCP, Electrophoresis 33, 3052–61 2012). For the MLPA-CE-SSCP based SLE CNV detection system, we also included 3 previously reported CNVs such as CCL3L1, FCGR3B, and EGR2. As a result, all the targets were well separated and the expected CNVs were consistently identified by the SLE MLPA-CE-SSCP system. After validation of the performance of SLE MLPA-CE-SSCP system, we applied the system for 113 SLEs and found that deletion of C4 was the most significantly associated with the risk of SLE. Our results suggest that the SLE MLPA-CE-SSCP system can be useful for predicting the risk of SLE. However, further larger scale study will be required.
Biography
Yeun-Jun Chung is a Professor of Medical Microbiology and Head of Integrated Research Center for Genome Polymorphism (Catholic Medical College, Korea). He has studied genomics based personalized medicine for past twenty years. Since he founded IRCGP, he has studied Variomics and Oncogenomics using array-CGH, GWAS, NGS, MLPA-CE-SSCP and BI tools. He has published >80 research papers including Gastroenterology, Genome Res, Arthritis Rheum, Cancer Res, Bioinformatics, J Pathol etc. Currently he is an editor-in-chief of Genomics & Informatics (official journal of Korean Genome Organization) and an Editorial Board Member of Experimental & Molecular Medicine and World Journal of Gastroenterology.
